Interpretive Summary: Common carp is an economically important food fish that has the longest history of domestication and is cultured worldwide. Fancy carp or koi are members of a subgroup of this species and are an important component of the U.S. aquaculture industry. Over the past few years, common carp and koi production enterprises have suffered from enormous losses due to disease outbreaks caused by cyprinid herpes virus-3 (CyHV-3). Analysis of gene polymorphisms and disease association is essential for assessing putative candidate genes affecting susceptibility or resistance to disease. We report the results of an association analysis between SNPs in common carp innate immune response genes and resistance to CyHV-3 infection. Our major finding is that DNA sequence polymorphism in the carp IL-10a gene is associated with disease resistance, although it is not clear yet if the association is affected directly by functional changes in the IL-10a protein or merely by the physical linkage of the IL-10a gene to other genes that affect resistance to the disease. Pending more research to validate the findings, this research will likely aid in developing molecular tools for breeding CyHV-3-resistant aquaculture stock, which will promote more sustainable production of common carp and the ornamental koi fish.

Technical Abstract:
Analysis of gene polymorphisms and disease association is essential for assessing putative candidate genes affecting susceptibility or resistance to disease. In this paper, we report the results of an association analysis between SNPs in common carp innate immune response genes and resistance to Cyprinid Herpes Virus - 3 (CyHV-3) infection. Twenty-three SNPs from 14 genes were genotyped in the progeny of a full-sib family, which was subjected to a CyHV-3 challenge. The challenge was carried out by cohabitation of naïve fish with CyHV-3-infected fish and the experimental fish subsequently were scored as susceptible or resistant. Fisher exact probability and chi-square tests were used to assess the association of SNP genotypes or alleles with CyHV-3 resistance. No association between SNPs in common carp immune response genes and resistance to CyHV-3 was found, except for SNPs in IL-10a. For IL-10a, both heterozygous and homozygous fish carrying the GCG haplotype were associated with CyHV-3 susceptibility (P < 0.001). To identify the source of susceptible and resistant alleles, we genotyped fish from the parental common carp strains. We found that the susceptible allele was more common among fish from the wild CyHV-3-resistant strain (Sassan) whereas the resistant allele was found in all the fish sampled from the susceptible domesticated strains (Našice and Dor-70). The implications of our findings to the development of a domesticated CyHV-3-resistant stock through marker-assisted selection or gene-introgression, and the possible impact of the IL-10a polymorphisms we identified on susceptibility to CyHV-3 infection in common carp are discussed.